Real-time predictive modelling
of epidemics


Sebastian Funk
15 March 2018
prowler.io, Cambridge

\begin{eqnarray} \dot{S}&=&-\beta \frac{S}{N}I\\ \dot{I}&=&+\beta \frac{S}{N}I - \gamma I\\ \dot{R}&=&+\gamma I \end{eqnarray}

What really happened

The unknown

  • Community/hospital/funeral transmission
  • Spatial dynamics
  • Changes in behaviour
  • Changes in reporting
  • Interventions
  • Seasonality
  • etc

The known

  • Average incubation period (~9 days)
  • Average infectious period (~11 days)
  • Case-fatality rate (~70%)

WHO Ebola response team (2014)

Transmission intensity as a stochastic process

\(d\log(\beta(t)) = \sigma dW_t\)

Dureau (2013)

Particle MCMC

  • Marginalise out stochastic process
  • Highly parallelisable

Andrieu (2010), Murray (2013)

Forecasting the Ebola epidemic in Western Area

Forecasting the Ebola epidemic in Western Area

Uses of real-time forecasts in outbreaks

  • Plan the scale of a response or intervention
  • Allocate resources (e.g., geographically)
  • Plan clinical trials

Assessing forecasts

Evaluating probabilistic forecasts requires
multiple observations.

Calibration: Compatibility of forecasts and observations.

Calibration: Compatibility of forecasts and observations.

Calibration: Compatibility of forecasts and observations.

"Evaluate predictive performance on the basis of maximising the sharpness of the predictive distribution subject to calibration"

Gneiting et al., J R Stat Soc B (2007)

Sharpness

Quality of forecasts vs quality of decisions

Outlook

Forecasts are becoming part of outbreak response

Forecasting challenges

Forecasting methodology is underdeveloped

Need methods to select the best model and
combine all available data streams
(individual/spatial/genetic/social)

Louis du Plessis, University of Oxford (unpublished)

New tools

New tools

Birch

Acknowledgements

Anton Camacho, Adam Kucharski, Roz Eggo, John Edmunds (LSHTM)
Bruce Reeder, Etienne Gignoux, Iza Ciglenecki, Amanda Tiffany (MSF)
James Hensman (prowler.io), Lawrence Murray (Uppsala)

Thank you!

http://sbfnk.github.io
@sbfnk